And one more thing The Web interface getting normal for some time after flush or delete the mail queues.

You need to look in the log files and see what's happening on your system. You also need to provide the specifications of your hardware. This looks like there's lots of mail in the queues, you need to find out why that's happening, check the log files. Have you made any changes to the anti-spam system or any other changes to Zimbra? Did you search the forums for similar problems?